diff --git a/.github/snapshots/gpu.nf.test.snap b/.github/snapshots/gpu.nf.test.snap index 8ab9a90bf6..5435135a0f 100644 --- a/.github/snapshots/gpu.nf.test.snap +++ b/.github/snapshots/gpu.nf.test.snap @@ -107,7 +107,7 @@ ], "meta": { "nf-test": "0.9.3", - "nextflow": "25.04.0" + "nextflow": "25.10.4" }, "timestamp": "2025-06-16T14:29:10.076573" } diff --git a/docs/api/_src/pipeline_lint_tests/container_configs.md b/docs/api/_src/pipeline_lint_tests/container_configs.md new file mode 100644 index 0000000000..491556d7ed --- /dev/null +++ b/docs/api/_src/pipeline_lint_tests/container_configs.md @@ -0,0 +1,5 @@ +# container_configs + + ```{eval-rst} + .. automethod:: nf_core.pipelines.lint.PipelineLint.container_configs + ``` diff --git a/docs/api/_src/pipeline_lint_tests/index.md b/docs/api/_src/pipeline_lint_tests/index.md index de0d97b788..5b1b72b0bb 100644 --- a/docs/api/_src/pipeline_lint_tests/index.md +++ b/docs/api/_src/pipeline_lint_tests/index.md @@ -5,6 +5,7 @@ - [actions_nf_test](./actions_nf_test/) - [actions_schema_validation](./actions_schema_validation/) - [base_config](./base_config/) + - [container_configs](./container_configs/) - [files_exist](./files_exist/) - [files_unchanged](./files_unchanged/) - [included_configs](./included_configs/) diff --git a/nf_core/components/install.py b/nf_core/components/install.py index 70cb95a929..8350159320 100644 --- a/nf_core/components/install.py +++ b/nf_core/components/install.py @@ -20,6 +20,7 @@ ) from nf_core.modules.modules_json import ModulesJson from nf_core.modules.modules_repo import ModulesRepo +from nf_core.pipelines.containers_utils import try_generate_container_configs log = logging.getLogger(__name__) @@ -158,7 +159,7 @@ def install(self, component: str | dict[str, str], silent: bool = False) -> bool if not self.install_component_files(component, version, self.modules_repo, install_folder): return False - # Update module.json with newly installed subworkflow + # Update module.json with newly installed component modules_json.load() modules_json.update( self.component_type, self.modules_repo, component, version, self.installed_by, install_track @@ -168,6 +169,10 @@ def install(self, component: str | dict[str, str], silent: bool = False) -> bool # Install included modules and subworkflows self.install_included_components(component_dir) + # Regenerate container configuration files for the pipeline when modules are installed + if self.component_type == "modules": + try_generate_container_configs(self.directory, component_dir, component) + if not silent: modules_json.load() modules_json.dump(run_prettier=True) diff --git a/nf_core/components/patch.py b/nf_core/components/patch.py index 2f3d29d992..f7a1a00b6f 100644 --- a/nf_core/components/patch.py +++ b/nf_core/components/patch.py @@ -9,6 +9,7 @@ from nf_core.components.components_command import ComponentCommand from nf_core.components.components_differ import ComponentsDiffer from nf_core.modules.modules_json import ModulesJson +from nf_core.pipelines.containers_utils import try_generate_container_configs log = logging.getLogger(__name__) @@ -118,7 +119,8 @@ def patch(self, component=None): ) # Write the patch to a temporary location (otherwise it is printed to the screen later) - patch_temp_path = tempfile.mktemp() + with tempfile.NamedTemporaryFile(delete=False) as tmp: + patch_temp_path = tmp.name try: ComponentsDiffer.write_diff_file( patch_temp_path, @@ -156,6 +158,10 @@ def patch(self, component=None): shutil.move(patch_temp_path, patch_path) log.info(f"Patch file of '{component_fullname}' written to '{patch_path}'") + # Regenerate container configuration files for the pipeline when modules are removed + if self.component_type == "modules": + try_generate_container_configs(self.directory) + def remove(self, component): # Check modules directory structure self.check_modules_structure() @@ -163,6 +169,8 @@ def remove(self, component): self.modules_json.check_up_to_date() self._parameter_checks(component) components = self.modules_json.get_all_components(self.component_type).get(self.modules_repo.remote_url) + if components is None: + raise ValueError(f"No components found for {self.component_type} in the pipeline") if component is None: self.require_prompts( diff --git a/nf_core/components/remove.py b/nf_core/components/remove.py index 1d34024920..123f0c6b52 100644 --- a/nf_core/components/remove.py +++ b/nf_core/components/remove.py @@ -9,6 +9,7 @@ import nf_core.utils from nf_core.components.components_command import ComponentCommand from nf_core.modules.modules_json import ModulesJson +from nf_core.pipelines.containers_utils import try_generate_container_configs from .install import ComponentInstall @@ -180,6 +181,10 @@ def remove(self, component, repo_url=None, repo_path=None, removed_by=None, remo # remember removed dependencies if dependency_removed: removed_components.append(component_name.replace("/", "_")) + # Regenerate container configuration files for the pipeline when modules are removed + if self.component_type == "modules": + try_generate_container_configs(self.directory) + # print removed dependencies dependencies = set(removed_components) - {component} if dependencies: diff --git a/nf_core/components/update.py b/nf_core/components/update.py index 4d05264449..e679643735 100644 --- a/nf_core/components/update.py +++ b/nf_core/components/update.py @@ -16,6 +16,7 @@ from nf_core.components.remove import ComponentRemove from nf_core.modules.modules_json import ModulesJson from nf_core.modules.modules_repo import ModulesRepo +from nf_core.pipelines.containers_utils import try_generate_container_configs from nf_core.utils import plural_es, plural_s, plural_y log = logging.getLogger(__name__) @@ -307,6 +308,10 @@ def update(self, component=None, silent=False, updated=None, check_diff_exist=Tr # Update modules.json with newly installed component self.modules_json.update(self.component_type, modules_repo, component, version, installed_by=None) updated.append(component) + + # Regenerate container configuration files for the pipeline when modules are updated + if self.component_type == "modules": + try_generate_container_configs(self.directory) recursive_update = True modules_to_update, subworkflows_to_update = self.get_components_to_update(component) if not silent and len(modules_to_update + subworkflows_to_update) > 0 and not self.update_all: diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json index 3f808a3522..cac8420ac2 100644 --- a/nf_core/pipeline-template/modules.json +++ b/nf_core/pipeline-template/modules.json @@ -8,12 +8,12 @@ {%- if fastqc %} "fastqc": { "branch": "master", - "git_sha": "3009f27c4e4b6e99da4eeebe82799e13924a4a1f", + "git_sha": "6d46786420b4d7bc88eba026eb389c0c5535d120", "installed_by": ["modules"] }{% endif %}{%- if multiqc %}{% if fastqc %},{% endif %} "multiqc": { "branch": "master", - "git_sha": "2c73cc8fa92cf48de3da0b643fdf357a8a290b36", + "git_sha": "008f9d3e61209bf995edac3ba531f54e269e1215", "installed_by": ["modules"] } {%- endif %} diff --git a/nf_core/pipeline-template/modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt b/nf_core/pipeline-template/modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt new file mode 100644 index 0000000000..7770ccd5fc --- /dev/null +++ b/nf_core/pipeline-template/modules/nf-core/fastqc/.conda-lock/linux_amd64-bd-5cb1a2fa2f18c7c2_1.txt @@ -0,0 +1,822 @@ + +version: 6 +environments: +default: +channels: +- url: https://conda.anaconda.org/conda-forge/ +- url: https://conda.anaconda.org/bioconda/ +- url: https://conda.anaconda.org/bioconda/ +options: +pypi-prerelease-mode: if-necessary-or-explicit +packages: +linux-64: +- conda: https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda +- conda: https://conda.anaconda.org/conda-forge/linux-64/alsa-lib-1.2.15.3-hb03c661_0.conda +- 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b/nf_core/pipeline-template/modules/nf-core/fastqc/main.nf @@ -3,35 +3,38 @@ process FASTQC { label 'process_low' conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' : - 'biocontainers/fastqc:0.12.1--hdfd78af_0' }" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' + : 'quay.io/biocontainers/fastqc:0.12.1--hdfd78af_0'}" input: - tuple val(meta), path(reads) + tuple val(meta), path(reads, stageAs: '?/*') output: - tuple val(meta) , path("*.html") , emit: html - tuple val(meta) , path("*.zip") , emit: zip + tuple val(meta), path("*.html"), emit: html + tuple val(meta), path("*.zip"), emit: zip tuple val("${task.process}"), val('fastqc'), eval('fastqc --version | sed "/FastQC v/!d; s/.*v//"'), emit: versions_fastqc, topic: versions when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" // Make list of old name and new name pairs to use for renaming in the bash while loop - def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] } - def rename_to = old_new_pairs*.join(' ').join(' ') - def renamed_files = old_new_pairs.collect{ _old_name, new_name -> new_name }.join(' ') + def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[reads, "${prefix}.${reads.extension}"]] : reads.withIndex().collect { entry, index -> [entry, "${prefix}_${index + 1}.${entry.extension}"] } + def rename_to = old_new_pairs*.join(' ').join(' ') + def renamed_files = old_new_pairs.collect { _old_name, new_name -> new_name }.join(' ') // The total amount of allocated RAM by FastQC is equal to the number of threads defined (--threads) time the amount of RAM defined (--memory) // https://github.com/s-andrews/FastQC/blob/1faeea0412093224d7f6a07f777fad60a5650795/fastqc#L211-L222 - // Dividing the task.memory by task.cpu allows to stick to requested amount of RAM in the label - def memory_in_mb = task.memory ? task.memory.toUnit('MB') / task.cpus : null + // Dividing the task.memory by task.cpus allows to stick to requested amount of RAM in the label + def memory_in_mb = task.memory + ? (task.memory.toUnit('MB') / task.cpus).intValue() + : null // FastQC memory value allowed range (100 - 10000) def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) + def fastqc_memory_arg = fastqc_memory ? "--memory ${fastqc_memory}" : '' """ printf "%s %s\\n" ${rename_to} | while read old_name new_name; do @@ -41,7 +44,7 @@ process FASTQC { fastqc \\ ${args} \\ --threads ${task.cpus} \\ - --memory ${fastqc_memory} \\ + ${fastqc_memory_arg} \\ ${renamed_files} """ diff --git a/nf_core/pipeline-template/modules/nf-core/fastqc/meta.yml b/nf_core/pipeline-template/modules/nf-core/fastqc/meta.yml index 49164c88fb..2f6cfef6d0 100644 --- a/nf_core/pipeline-template/modules/nf-core/fastqc/meta.yml +++ b/nf_core/pipeline-template/modules/nf-core/fastqc/meta.yml @@ -86,26 +86,26 @@ maintainers: - "@ewels" - "@FelixKrueger" containers: - conda: - linux_amd64: - lock_file: https://wave.seqera.io/v1alpha1/builds/bd-af7a5314d5015c29_1/condalock - linux_arm64: - lock_file: https://wave.seqera.io/v1alpha1/builds/bd-df99cb252670875a_2/condalock docker: - linux_amd64: - build_id: bd-af7a5314d5015c29_1 - name: community.wave.seqera.io/library/fastqc:0.12.1--af7a5314d5015c29 - scanId: sc-a618548acbee5a8a_30 - linux_arm64: - build_id: bd-df99cb252670875a_2 - name: community.wave.seqera.io/library/fastqc:0.12.1--df99cb252670875a - scanId: sc-b5913ed5d42b22d2_18 + linux/arm64: + name: community.wave.seqera.io/library/fastqc:0.12.1--e455e32f745abe68 + build_id: bd-e455e32f745abe68_1 + scan_id: sc-f102f736465af88c_1 + linux/amd64: + name: community.wave.seqera.io/library/fastqc:0.12.1--5cb1a2fa2f18c7c2 + build_id: bd-5cb1a2fa2f18c7c2_1 + scan_id: sc-0c0466326b6b77d2_1 singularity: - linux_amd64: - build_id: bd-104d26ddd9519960_1 - name: oras://community.wave.seqera.io/library/fastqc:0.12.1--104d26ddd9519960 - https: https://community.wave.seqera.io/v2/library/fastqc/blobs/sha256:e0c976cb2eca5fee72618a581537a4f8ea42fcae24c9b201e2e0f764fd28648a - linux_arm64: - build_id: bd-d56b505a93aef38a_1 - name: oras://community.wave.seqera.io/library/fastqc:0.12.1--d56b505a93aef38a - https: 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+# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-64/libgomp-15.2.0-he0feb66_18.conda#239c5e9546c38a1e884d69effcf4c882 +https://conda.anaconda.org/conda-forge/linux-64/_openmp_mutex-4.5-20_gnu.conda#a9f577daf3de00bca7c3c76c0ecbd1de +https://conda.anaconda.org/conda-forge/linux-64/libgcc-15.2.0-he0feb66_18.conda#0aa00f03f9e39fb9876085dee11a85d4 +https://conda.anaconda.org/conda-forge/linux-64/bzip2-1.0.8-hda65f42_9.conda#d2ffd7602c02f2b316fd921d39876885 +https://conda.anaconda.org/conda-forge/linux-64/libzlib-1.3.2-h25fd6f3_2.conda#d87ff7921124eccd67248aa483c23fec +https://conda.anaconda.org/conda-forge/linux-64/zstd-1.5.7-hb78ec9c_6.conda#4a13eeac0b5c8e5b8ab496e6c4ddd829 +https://conda.anaconda.org/conda-forge/linux-64/ld_impl_linux-64-2.45.1-default_hbd61a6d_102.conda#18335a698559cdbcd86150a48bf54ba6 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b/nf_core/pipeline-template/modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt @@ -0,0 +1,125 @@ + +# This file may be used to create an environment using: +# $ conda create --name --file +# platform: linux-aarch64 +@EXPLICIT +https://conda.anaconda.org/conda-forge/linux-aarch64/libgomp-15.2.0-h8acb6b2_18.conda#4faa39bf919939602e594253bd673958 +https://conda.anaconda.org/conda-forge/linux-aarch64/_openmp_mutex-4.5-20_gnu.conda#468fd3bb9e1f671d36c2cbc677e56f1d +https://conda.anaconda.org/conda-forge/linux-aarch64/libgcc-15.2.0-h8acb6b2_18.conda#552567ea2b61e3a3035759b2fdb3f9a6 +https://conda.anaconda.org/conda-forge/linux-aarch64/bzip2-1.0.8-h4777abc_9.conda#840d8fc0d7b3209be93080bc20e07f2d +https://conda.anaconda.org/conda-forge/linux-aarch64/libzlib-1.3.2-hdc9db2a_2.conda#502006882cf5461adced436e410046d1 +https://conda.anaconda.org/conda-forge/linux-aarch64/zstd-1.5.7-h85ac4a6_6.conda#c3655f82dcea2aa179b291e7099c1fcc 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+https://conda.anaconda.org/conda-forge/noarch/typing-inspection-0.4.2-pyhd8ed1ab_1.conda#a0a4a3035667fc34f29bfbd5c190baa6 +https://conda.anaconda.org/conda-forge/noarch/pydantic-2.13.3-pyhcf101f3_0.conda#f690e6f204efd2e5c06b57518a383d98 +https://conda.anaconda.org/conda-forge/noarch/python-dotenv-1.2.2-pyhcf101f3_0.conda#130584ad9f3a513cdd71b1fdc1244e9c +https://conda.anaconda.org/conda-forge/noarch/python-kaleido-0.2.1-pyhd8ed1ab_0.tar.bz2#310259a5b03ff02289d7705f39e2b1d2 +https://conda.anaconda.org/conda-forge/noarch/pysocks-1.7.1-pyha55dd90_7.conda#461219d1a5bd61342293efa2c0c90eac +https://conda.anaconda.org/conda-forge/noarch/urllib3-2.6.3-pyhd8ed1ab_0.conda#9272daa869e03efe68833e3dc7a02130 +https://conda.anaconda.org/conda-forge/noarch/requests-2.33.1-pyhcf101f3_0.conda#10afbb4dbf06ff959ad25a92ccee6e59 +https://conda.anaconda.org/conda-forge/noarch/pygments-2.20.0-pyhd8ed1ab_0.conda#16c18772b340887160c79a6acc022db0 +https://conda.anaconda.org/conda-forge/noarch/rich-15.0.0-pyhcf101f3_0.conda#0242025a3c804966bf71aa04eee82f66 +https://conda.anaconda.org/conda-forge/noarch/rich-click-1.9.7-pyh8f84b5b_0.conda#0c20a8ebcddb24a45da89d5e917e6cb9 +https://conda.anaconda.org/conda-forge/noarch/spectra-0.0.11-pyhd8ed1ab_2.conda#472239e4eb7b5a84bb96b3ed7e3a596a +https://conda.anaconda.org/conda-forge/linux-aarch64/regex-2026.4.4-py314h51f160d_0.conda#88a3dbd279e6b1faf0cddb8397866864 +https://conda.anaconda.org/conda-forge/linux-aarch64/tiktoken-0.12.0-py314h6a36e60_3.conda#55bf7b559202236157b14323b40f19e6 +https://conda.anaconda.org/conda-forge/noarch/tqdm-4.67.3-pyh8f84b5b_0.conda#e5ce43272193b38c2e9037446c1d9206 +https://conda.anaconda.org/conda-forge/noarch/typeguard-4.5.1-pyhd8ed1ab_0.conda#260af1b0a94f719de76b4e14094e9a3b +https://conda.anaconda.org/bioconda/noarch/multiqc-1.34-pyhdfd78af_0.conda#a7111ab9a6a6146b40cbce16655ac873 +https://conda.anaconda.org/conda-forge/noarch/pip-26.0.1-pyh145f28c_0.conda#09a970fbf75e8ed1aa633827ded6aa4f +https://conda.anaconda.org/conda-forge/linux-aarch64/procps-ng-4.0.6-h1779866_0.conda#ab7288cc39545556d1bc5e71ab2df9a9 diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml b/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml index 009874d4c0..37e7612d4c 100644 --- a/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml +++ b/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml @@ -4,4 +4,4 @@ channels: - conda-forge - bioconda dependencies: - - bioconda::multiqc=1.33 + - bioconda::multiqc=1.34 diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf b/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf index 5376aea1ed..e80e8cd8d1 100644 --- a/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf +++ b/nf_core/pipeline-template/modules/nf-core/multiqc/main.nf @@ -3,9 +3,9 @@ process MULTIQC { label 'process_single' conda "${moduleDir}/environment.yml" - container "${workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container - ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/34/34e733a9ae16a27e80fe00f863ea1479c96416017f24a907996126283e7ecd4d/data' - : 'community.wave.seqera.io/library/multiqc:1.33--ee7739d47738383b'}" + container "${workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container + ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data' + : 'community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6'}" input: tuple val(meta), path(multiqc_files, stageAs: "?/*"), path(multiqc_config, stageAs: "?/*"), path(multiqc_logo), path(replace_names), path(sample_names) diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/meta.yml b/nf_core/pipeline-template/modules/nf-core/multiqc/meta.yml index ef434a9a23..2facc627ba 100644 --- a/nf_core/pipeline-template/modules/nf-core/multiqc/meta.yml +++ b/nf_core/pipeline-template/modules/nf-core/multiqc/meta.yml @@ -110,24 +110,24 @@ maintainers: containers: conda: linux/amd64: - lock_file: https://wave.seqera.io/v1alpha1/builds/bd-ee7739d47738383b_1/condalock + lock_file: modules/nf-core/multiqc/.conda-lock/linux_amd64-bd-db7c73dae76bc9e6_1.txt linux/arm64: - lock_file: https://wave.seqera.io/v1alpha1/builds/bd-58d7dee710ab3aa8_1/condalock + lock_file: modules/nf-core/multiqc/.conda-lock/linux_arm64-bd-d167b8012595a136_1.txt docker: linux/amd64: - build_id: bd-ee7739d47738383b_1 - name: community.wave.seqera.io/library/multiqc:1.33--ee7739d47738383b - scanId: sc-6ddec592dcadd583_4 + name: community.wave.seqera.io/library/multiqc:1.34--db7c73dae76bc9e6 + build_id: bd-db7c73dae76bc9e6_1 + scan_id: sc-66fc7138dbf1cf48_1 linux/arm64: - build_id: bd-58d7dee710ab3aa8_1 - name: community.wave.seqera.io/library/multiqc:1.33--58d7dee710ab3aa8 - scanId: sc-a04c42273e34c55c_2 + name: community.wave.seqera.io/library/multiqc:1.34--d167b8012595a136 + build_id: bd-d167b8012595a136_1 + scan_id: sc-ac701dfa631a2af9_1 singularity: linux/amd64: - build_id: bd-e3576ddf588fa00d_1 - https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/34/34e733a9ae16a27e80fe00f863ea1479c96416017f24a907996126283e7ecd4d/data - name: oras://community.wave.seqera.io/library/multiqc:1.33--e3576ddf588fa00d + name: oras://community.wave.seqera.io/library/multiqc:1.34--4fc8657c816047c0 + build_id: bd-4fc8657c816047c0_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/1b/1bef8af6be88c5733461959c46ac8ef73d18f65277f62a1695d0e1633054f9c2/data linux/arm64: - build_id: bd-2537ca5f8445e3c2_1 - https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/78/78b89e91d89e9cc99ad5ade5be311f347838cb2acbfb4f13bc343b170be09ce4/data - name: oras://community.wave.seqera.io/library/multiqc:1.33--2537ca5f8445e3c2 + name: oras://community.wave.seqera.io/library/multiqc:1.34--7fbd82d945c06726 + build_id: bd-7fbd82d945c06726_1 + https: https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/9a/9a1fec9662a152683e6fcae440d0ce20920b3b89dc62d1e3a52e73f92eba0969/data diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test b/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test index 0e422eaa6c..4cbdb95d43 100644 --- a/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test +++ b/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test @@ -29,13 +29,26 @@ nextflow_process { then { assert process.success - assertAll( - { assert snapshot( - file(process.out.report[0][1]).name, - file(process.out.data[0][1]).name, - process.out.findAll { key, val -> key.startsWith("versions") - }).match() } - ) + assert snapshot( + sanitizeOutput(process.out).collectEntries { key, val -> + if (key == "data") { + return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] + } + else if (key == "plots") { + return [key, val.collect { [ + "pdf", + path("${it[1]}/pdf").list().collect { file(it.toString()).name }, + "png", + path("${it[1]}/png").list().collect { file(it.toString()).name }, + "svg", + path("${it[1]}/svg").list().collect { file(it.toString()).name }] }] + } + else if (key == "report") { + return [key, file(val[0][1].toString()).name] + } + return [key, val] + } + ).match() } } @@ -59,13 +72,26 @@ nextflow_process { then { assert process.success - assertAll( - { assert snapshot( - file(process.out.report[0][1]).name, - file(process.out.data[0][1]).name, - process.out.findAll { key, val -> key.startsWith("versions") - }).match() } - ) + assert snapshot( + sanitizeOutput(process.out).collectEntries { key, val -> + if (key == "data") { + return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] + } + else if (key == "plots") { + return [key, val.collect { [ + "pdf", + path("${it[1]}/pdf").list().collect { file(it.toString()).name }, + "png", + path("${it[1]}/png").list().collect { file(it.toString()).name }, + "svg", + path("${it[1]}/svg").list().collect { file(it.toString()).name }] }] + } + else if (key == "report") { + return [key, file(val[0][1].toString()).name] + } + return [key, val] + } + ).match() } } @@ -77,7 +103,7 @@ nextflow_process { input[0] = channel.of([ [ id: 'FASTQC' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), - file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true), + file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true), [], [], [] @@ -88,14 +114,26 @@ nextflow_process { then { assert process.success - assertAll( - { assert snapshot( - file(process.out.report[0][1]).name, - file(process.out.data[0][1]).name, - file(process.out.plots[0][1]).name, - process.out.findAll { key, val -> key.startsWith("versions") - }).match() } - ) + assert snapshot( + sanitizeOutput(process.out).collectEntries { key, val -> + if (key == "data") { + return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] + } + else if (key == "plots") { + return [key, val.collect { [ + "pdf", + path("${it[1]}/pdf").list().collect { file(it.toString()).name }, + "png", + path("${it[1]}/png").list().collect { file(it.toString()).name }, + "svg", + path("${it[1]}/svg").list().collect { file(it.toString()).name }] }] + } + else if (key == "report") { + return [key, file(val[0][1].toString()).name] + } + return [key, val] + } + ).match() } } @@ -108,8 +146,8 @@ nextflow_process { [ id: 'FASTQC' ], file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true), [ - file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true), - file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true) + file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true), + file("https://raw.githubusercontent.com/nf-core/seqinspector/1.0.0/assets/multiqc_config.yml", checkIfExists: true) ], [], [], @@ -121,14 +159,26 @@ nextflow_process { then { assert process.success - assertAll( - { assert snapshot( - file(process.out.report[0][1]).name, - file(process.out.data[0][1]).name, - file(process.out.plots[0][1]).name, - process.out.findAll { key, val -> key.startsWith("versions") - }).match() } - ) + assert snapshot( + sanitizeOutput(process.out).collectEntries { key, val -> + if (key == "data") { + return [key, val.collect { [path(it[1]).list().collect { file(it.toString()).name }] }] + } + else if (key == "plots") { + return [key, val.collect { [ + "pdf", + path("${it[1]}/pdf").list().collect { file(it.toString()).name }, + "png", + path("${it[1]}/png").list().collect { file(it.toString()).name }, + "svg", + path("${it[1]}/svg").list().collect { file(it.toString()).name }] }] + } + else if (key == "report") { + return [key, file(val[0][1].toString()).name] + } + return [key, val] + } + ).match() } } diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap b/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap index c022701f74..7c2f370f39 100644 --- a/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap +++ b/nf_core/pipeline-template/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -1,44 +1,190 @@ { "sarscov2 single-end [fastqc] [multiple configs]": { "content": [ - "multiqc_report.html", - "multiqc_data", - "multiqc_plots", { + "data": [ + [ + [ + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "llms-full.txt", + "multiqc.log", + "multiqc.parquet", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_sources.txt" + ] + ] + ], + "plots": [ + [ + "pdf", + [ + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf" + ], + "png", + [ + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png" + ], + "svg", + [ + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg" + ] + ] + ], + "report": "multiqc_report.html", "versions": [ [ "MULTIQC", "multiqc", - "1.33" + "1.34" ] ] } ], + "timestamp": "2026-03-17T16:15:42.577775492", "meta": { - "nf-test": "0.9.3", + "nf-test": "0.9.4", "nextflow": "25.10.4" - }, - "timestamp": "2026-02-26T20:21:35.851707" + } }, "sarscov2 single-end [fastqc]": { "content": [ - "multiqc_report.html", - "multiqc_data", { + "data": [ + [ + [ + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "llms-full.txt", + "multiqc.log", + "multiqc.parquet", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_software_versions.txt", + "multiqc_sources.txt" + ] + ] + ], + "plots": [ + [ + "pdf", + [ + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf" + ], + "png", + [ + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png" + ], + "svg", + [ + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg" + ] + ] + ], + "report": "multiqc_report.html", "versions": [ [ "MULTIQC", "multiqc", - "1.33" + "1.34" ] ] } ], + "timestamp": "2026-03-17T16:21:17.072841555", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" - }, - "timestamp": "2026-02-26T15:10:36.019680076" + } }, "sarscov2 single-end [fastqc] - stub": { "content": [ @@ -75,56 +221,202 @@ [ "MULTIQC", "multiqc", - "1.33" + "1.34" ] ] } ], + "timestamp": "2026-02-26T15:14:39.789193051", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" - }, - "timestamp": "2026-02-26T15:14:39.789193051" + } }, "sarscov2 single-end [fastqc] [config]": { "content": [ - "multiqc_report.html", - "multiqc_data", - "multiqc_plots", { + "data": [ + [ + [ + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "llms-full.txt", + "multiqc.log", + "multiqc.parquet", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_sources.txt" + ] + ] + ], + "plots": [ + [ + "pdf", + [ + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf" + ], + "png", + [ + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png" + ], + "svg", + [ + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg" + ] + ] + ], + "report": "multiqc_report.html", "versions": [ [ "MULTIQC", "multiqc", - "1.33" + "1.34" ] ] } ], + "timestamp": "2026-03-17T16:15:30.372239611", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" - }, - "timestamp": "2026-02-26T15:21:29.116129274" + } }, "sarscov2 single-end [fastqc] - custom prefix": { "content": [ - "custom_prefix.html", - "custom_prefix_data", { + "data": [ + [ + [ + "fastqc-status-check-heatmap.txt", + "fastqc_overrepresented_sequences_plot.txt", + "fastqc_per_base_n_content_plot.txt", + "fastqc_per_base_sequence_quality_plot.txt", + "fastqc_per_sequence_gc_content_plot_Counts.txt", + "fastqc_per_sequence_gc_content_plot_Percentages.txt", + "fastqc_per_sequence_quality_scores_plot.txt", + "fastqc_sequence_counts_plot.txt", + "fastqc_sequence_duplication_levels_plot.txt", + "fastqc_sequence_length_distribution_plot.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "llms-full.txt", + "multiqc.log", + "multiqc.parquet", + "multiqc_citations.txt", + "multiqc_data.json", + "multiqc_fastqc.txt", + "multiqc_general_stats.txt", + "multiqc_software_versions.txt", + "multiqc_sources.txt" + ] + ] + ], + "plots": [ + [ + "pdf", + [ + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf" + ], + "png", + [ + "fastqc-status-check-heatmap.png", + "fastqc_overrepresented_sequences_plot.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_per_sequence_gc_content_plot_Counts.png", + "fastqc_per_sequence_gc_content_plot_Percentages.png", + "fastqc_per_sequence_quality_scores_plot.png", + "fastqc_sequence_counts_plot-cnt.png", + "fastqc_sequence_counts_plot-pct.png", + "fastqc_sequence_duplication_levels_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png" + ], + "svg", + [ + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg" + ] + ] + ], + "report": "custom_prefix.html", "versions": [ [ "MULTIQC", "multiqc", - "1.33" + "1.34" ] ] } ], + "timestamp": "2026-03-17T16:15:18.189023981", "meta": { "nf-test": "0.9.4", "nextflow": "25.10.4" - }, - "timestamp": "2026-02-26T15:10:43.419877592" + } } } \ No newline at end of file diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/tests/nextflow.config b/nf_core/pipeline-template/modules/nf-core/multiqc/tests/nextflow.config index c537a6a3e7..374dfef2c7 100644 --- a/nf_core/pipeline-template/modules/nf-core/multiqc/tests/nextflow.config +++ b/nf_core/pipeline-template/modules/nf-core/multiqc/tests/nextflow.config @@ -1,5 +1,6 @@ process { withName: 'MULTIQC' { ext.prefix = null + ext.args = '-p' } } diff --git a/nf_core/pipelines/containers_utils.py b/nf_core/pipelines/containers_utils.py new file mode 100644 index 0000000000..af64f9582f --- /dev/null +++ b/nf_core/pipelines/containers_utils.py @@ -0,0 +1,195 @@ +import json +import logging +import re +from pathlib import Path + +import yaml + +from nf_core.utils import NF_INSPECT_MIN_NF_VERSION, check_nextflow_version, pretty_nf_version, run_cmd + +log = logging.getLogger(__name__) + +PLATFORMS: dict[str, list[str]] = { + "docker_amd64": ["docker", "linux/amd64", "name"], + "docker_arm64": ["docker", "linux/arm64", "name"], + "singularity_oras_amd64": ["singularity", "linux/amd64", "name"], + "singularity_oras_arm64": ["singularity", "linux/arm64", "name"], + "singularity_https_amd64": ["singularity", "linux/amd64", "https"], + "singularity_https_arm64": ["singularity", "linux/arm64", "https"], + "conda_lock_files_amd64": ["conda", "linux/amd64", "lock_file"], + "conda_lock_files_arm64": ["conda", "linux/arm64", "lock_file"], +} + + +class ContainerConfigs: + """Generates the container configuration files for a pipeline. + + Args: + workflow_directory (Path): The directory containing the workflow files. + """ + + def __init__( + self, + workflow_directory: Path = Path(), + ): + self.workflow_directory = workflow_directory + + def check_nextflow_version_sufficient(self) -> None: + """Check if the Nextflow version is sufficient to run `nextflow inspect`.""" + if not check_nextflow_version(NF_INSPECT_MIN_NF_VERSION, silent=True): + raise UserWarning( + f"To use Seqera containers Nextflow version >= {pretty_nf_version(NF_INSPECT_MIN_NF_VERSION)} is required.\n" + f"Please update your Nextflow version with [magenta]'nextflow self-update'[/]\n" + ) + + def parse_module_paths(self) -> dict[str, Path]: + """Parse include statements from workflow files to extract module paths. + + Only processes includes pointing to 'modules/' directories. + Extracts the path from 'modules/' onwards, ignoring any '../' prefixes. + + Returns: + dict: Mapping of process names to their module paths (e.g., 'modules/nf-core/fastqc') + """ + module_paths = {} + + # Pattern matches: include { NAME ... } from 'path' + # Captures the first name (original) and the path, ignoring any alias + include_pattern = re.compile(r"include\s*\{\s*(\w+).*?\}\s*from\s+['\"]([^'\"]+)['\"]") + + # Search in workflows, modules, and subworkflows directories + search_dirs = ["workflows", "modules", "subworkflows"] + + for search_dir in search_dirs: + search_path = self.workflow_directory / search_dir + if not search_path.exists(): + continue + + for nf_file in search_path.rglob("*.nf"): + try: + content = nf_file.read_text() + for match in include_pattern.finditer(content): + process_name = match.group(1) + relative_path = match.group(2) + + # Only process paths that contain 'modules/' + if "modules/" not in relative_path: + continue + + # Extract everything from 'modules/' onwards, removing any '/main' suffix + module_path_str = relative_path[relative_path.find("modules/") :] + module_path_str = module_path_str.replace("/main", "") + + module_paths[process_name] = Path(module_path_str) + log.debug(f"Found include: {process_name} -> {module_path_str}") + + except OSError as e: + log.debug(f"Error parsing {nf_file}: {e}") + continue + + return module_paths + + def generate_container_configs( + self, new_module_path: Path | None = None, new_module_name: str | None = None + ) -> set[str]: + """ + Generate the container configuration files for a pipeline. + Requires Nextflow >= 25.04.4 + + Returns: + set[str]: Names of config files written (e.g. ``{'containers_docker_amd64.config'}``). + """ + self.check_nextflow_version_sufficient() + log.debug("Generating container config file with [magenta bold]nextflow inspect[/].") + try: + # Run nextflow inspect + executable = "nextflow" + cmd_params = f"inspect -format json {self.workflow_directory}" + cmd_out = run_cmd(executable, cmd_params) + if cmd_out is None: + raise UserWarning("Failed to run `nextflow inspect`. Please check your Nextflow installation.") + + out, _ = cmd_out + out_json = json.loads(out) + + except RuntimeError as e: + log.error("Running 'nextflow inspect' failed with the following error:") + raise UserWarning(e) from e + + module_names = {p.get("name") for p in out_json["processes"] if p.get("name")} + log.debug(f"Found {len(module_names)} modules: {', '.join(module_names)}") + + # Parse module paths from include statements + module_path_map = self.parse_module_paths() + log.debug(f"Parsed {len(module_path_map)} module paths from include statements") + + if new_module_name and new_module_path: + module_names.add(new_module_name.upper()) + module_path_map[new_module_name.upper()] = new_module_path + + # Build containers dict from module meta.yml files + # Pre-initialize all platforms to avoid repeated existence checks + has_warnings = False + containers: dict[str, dict[str, str]] = {platform: {} for platform in PLATFORMS} + for m_name in module_names: + # Try to get module path from include statements + if m_name in module_path_map: + module_path = module_path_map[m_name] + log.debug(f"Using parsed path for {m_name}: {module_path}") + else: + # Fallback to old heuristic method + log.debug(f"No parsed path found for {m_name}, using heuristic") + module_path = Path(*m_name.lower().split("_", 1)) + + # Look for meta.yml in the module path + meta_path = self.workflow_directory / module_path / "meta.yml" + + try: + with open(meta_path) as fh: + meta = yaml.safe_load(fh) + log.debug(f"Loaded meta.yml for {m_name} from {meta_path}") + except FileNotFoundError: + log.warning(f"Could not find meta.yml for {m_name} at {meta_path}") + continue + + # Extract containers for all platforms + for platform_name, (runtime, arch, protocol) in PLATFORMS.items(): + try: + containers[platform_name][m_name] = meta["containers"][runtime][arch][protocol] + log.debug(f"Found {platform_name} container for {m_name}") + except (KeyError, TypeError): + log.debug(f"Could not find {platform_name} container for {m_name}") + has_warnings = True + continue + if has_warnings: + log.info( + "Generated container configs for the pipeline. Not all containers were found. Run with `-v` to see detailed warning messages." + ) + else: + log.info("Generated container configs for the pipeline successfully.") + + # remove all generated config files, to handle removed modules + for platform in PLATFORMS: + (self.workflow_directory / "conf" / f"containers_{platform}.config").unlink(missing_ok=True) + # write config files + written: set[str] = set() + for platform, module_containers in containers.items(): + if not module_containers: + continue + lines = [ + f"process {{ withName: '{module_name}' {{ container = '{container}' }} }}\n" + for module_name, container in sorted(module_containers.items()) + ] + config_path = self.workflow_directory / "conf" / f"containers_{platform}.config" + config_path.write_text("".join(lines)) + written.add(config_path.name) + return written + + +def try_generate_container_configs( + directory: Path, new_module_path: Path | None = None, new_module_name: str | None = None +) -> None: + try: + ContainerConfigs(directory).generate_container_configs(new_module_path, new_module_name) + except UserWarning as e: + log.warning(f"Could not regenerate container configuration files: {e}") diff --git a/nf_core/pipelines/create/create.py b/nf_core/pipelines/create/create.py index 055e5ae5bd..b1b9f45594 100644 --- a/nf_core/pipelines/create/create.py +++ b/nf_core/pipelines/create/create.py @@ -16,6 +16,7 @@ import nf_core import nf_core.utils +from nf_core.pipelines.containers_utils import try_generate_container_configs from nf_core.pipelines.create.utils import CreateConfig, features_yml_path, load_features_yaml from nf_core.pipelines.create_logo import create_logo from nf_core.pipelines.lint_utils import run_prettier_on_file @@ -328,8 +329,7 @@ def render_template(self) -> None: for template_fn_path in template_files: # Skip files that are in the self.skip_paths list for skip_path in self.skip_paths: - # TODO: Use Path.parts instead of str().startswith() to avoid unnecessary string conversion - if str(template_fn_path.relative_to(template_dir)).startswith(skip_path): + if template_fn_path.relative_to(template_dir).is_relative_to(skip_path): break else: if template_fn_path.is_dir(): @@ -394,6 +394,9 @@ def render_template(self) -> None: yaml.dump(config_yml.model_dump(exclude_none=True), fh, Dumper=custom_yaml_dumper()) log.debug(f"Dumping pipeline template yml to pipeline config file '{config_fn.name}'") + # generate container configs + try_generate_container_configs(self.outdir) + # Run prettier on files for pipelines sync log.debug("Running prettier on pipeline files") run_prettier_on_file([str(f) for f in self.outdir.glob("**/*")]) diff --git a/nf_core/pipelines/lint/__init__.py b/nf_core/pipelines/lint/__init__.py index dc17996be2..4cfe23ea69 100644 --- a/nf_core/pipelines/lint/__init__.py +++ b/nf_core/pipelines/lint/__init__.py @@ -34,6 +34,7 @@ from .actions_nf_test import actions_nf_test from .actions_schema_validation import actions_schema_validation from .configs import base_config, modules_config +from .container_configs import container_configs from .files_exist import files_exist from .files_unchanged import files_unchanged from .included_configs import included_configs @@ -87,6 +88,7 @@ class PipelineLint(nf_core.utils.Pipeline): actions_schema_validation = actions_schema_validation base_config = base_config modules_config = modules_config + container_configs = container_configs files_exist = files_exist files_unchanged = files_unchanged merge_markers = merge_markers @@ -166,6 +168,7 @@ def _get_all_lint_tests(release_mode): "modules_config", "nfcore_yml", "rocrate_readme_sync", + "container_configs", ] + (["version_consistency", "included_configs"] if release_mode else []) def _load(self) -> bool: diff --git a/nf_core/pipelines/lint/container_configs.py b/nf_core/pipelines/lint/container_configs.py new file mode 100644 index 0000000000..b5143dba82 --- /dev/null +++ b/nf_core/pipelines/lint/container_configs.py @@ -0,0 +1,78 @@ +import logging +from pathlib import Path + +import git + +from nf_core.pipelines.containers_utils import ContainerConfigs + +log = logging.getLogger(__name__) + + +def container_configs(self): + """Check that the container configuration files in ``conf/`` are up to date. + + Runs ``nextflow inspect`` to regenerate container configuration files directly + in ``conf/`` and uses ``git diff`` to detect changes. If not in ``--fix`` mode + the working tree is restored to its original state afterwards. + + Can be skipped by adding the following to the ``.nf-core.yml`` file: + + .. code-block:: yaml + + lint: + container_configs: False + """ + passed = [] + failed = [] + warned = [] + fixed = [] + could_fix = False + + conf_dir = Path(self.wf_path) / "conf" + repo = git.Repo(self.wf_path) + + try: + generated = ContainerConfigs(self.wf_path).generate_container_configs() + except UserWarning as e: + warned.append(f"Could not generate container configuration files: {e}") + return {"passed": passed, "failed": failed, "warned": warned} + + # Files modified in the working tree (tracked and changed by generation) + modified = { + Path(d.a_path).name + for d in repo.index.diff(None) + if d.a_path and Path(d.a_path).parent.name == "conf" and Path(d.a_path).name.startswith("containers_") + } + # Newly created files (generated but not previously tracked) + new = { + Path(f).name + for f in repo.untracked_files + if Path(f).parent.name == "conf" and Path(f).name.startswith("containers_") + } + # Already-correct files: generated, tracked, and unchanged + correct = generated - modified - new + + fixing = "container_configs" in self.fix + + for name in sorted(correct): + passed.append(f"`conf/{name}` is up to date") + + for name in sorted(modified | new): + if fixing: + passed.append(f"`conf/{name}` is up to date") + fixed.append(f"`conf/{name}` overwritten with regenerated container configuration.") + else: + if name in new: + failed.append(f"`conf/{name}` is missing – please regenerate the container configuration files.") + else: + failed.append(f"`conf/{name}` is out of date – please regenerate the container configuration files.") + could_fix = True + + if not fixing: + # Restore working tree: reset modified tracked files and delete new untracked ones + for name in modified: + repo.git.restore(str(conf_dir / name)) + for name in new: + (conf_dir / name).unlink(missing_ok=True) + + return {"passed": passed, "failed": failed, "warned": warned, "fixed": fixed, "could_fix": could_fix} diff --git a/nf_core/utils.py b/nf_core/utils.py index bac78de090..55f2ad3447 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -1370,6 +1370,8 @@ class NFCoreYamlLintConfig(BaseModel): """ Lint for included configs """ local_component_structure: bool | None = None """ Lint local components use correct structure mirroring remote""" + container_configs: bool | None = None + """ Lint that container configuration files in conf/ are up to date """ rocrate_readme_sync: bool | None = None """ Lint for README.md and rocrate.json sync """ diff --git a/tests/pipelines/lint/test_container_configs.py b/tests/pipelines/lint/test_container_configs.py new file mode 100644 index 0000000000..4610980466 --- /dev/null +++ b/tests/pipelines/lint/test_container_configs.py @@ -0,0 +1,134 @@ +from pathlib import Path +from unittest.mock import patch + +import git + +import nf_core.pipelines.lint + +from ..test_lint import TestLint + + +class TestLintContainerConfigs(TestLint): + def setUp(self) -> None: + super().setUp() + self.new_pipeline = self._make_pipeline_copy() + + # ------------------------------------------------------------------ + # helpers + # ------------------------------------------------------------------ + + def _lint(self): + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline) + lint_obj._load() + return lint_obj.container_configs() + + def _write_container_cfg(self, name: str, content: str) -> Path: + path = Path(self.new_pipeline) / "conf" / name + path.write_text(content) + return path + + def _commit_container_cfg(self, name: str, content: str) -> Path: + """Write and git-commit a container config so it shows up in ``git ls-files``.""" + path = self._write_container_cfg(name, content) + repo = git.Repo(self.new_pipeline) + repo.index.add([str(path)]) + repo.index.commit(f"Add {name} for testing") + return path + + # ------------------------------------------------------------------ + # tests + # ------------------------------------------------------------------ + + def test_container_configs_up_to_date(self): + """Linting passes when generated configs match what is on disk.""" + content = "process { withName: 'FASTQC' { container = 'docker.io/biocontainers/fastqc:0.12.1' } }\n" + self._commit_container_cfg("containers_docker_amd64.config", content) + + def generate(cc_self): + (cc_self.workflow_directory / "conf" / "containers_docker_amd64.config").write_text(content) + return {"containers_docker_amd64.config"} + + with patch( + "nf_core.pipelines.containers_utils.ContainerConfigs.generate_container_configs", + autospec=True, + side_effect=generate, + ): + result = self._lint() + + assert len(result["failed"]) == 0 + assert any("up to date" in p for p in result["passed"]) + + def test_container_configs_out_of_date(self): + """Linting fails when generated configs differ from what is on disk.""" + old = "process { withName: 'FASTQC' { container = 'old_image' } }\n" + new = "process { withName: 'FASTQC' { container = 'new_image' } }\n" + self._commit_container_cfg("containers_docker_amd64.config", old) + + def generate(cc_self): + (cc_self.workflow_directory / "conf" / "containers_docker_amd64.config").write_text(new) + return {"containers_docker_amd64.config"} + + with patch( + "nf_core.pipelines.containers_utils.ContainerConfigs.generate_container_configs", + autospec=True, + side_effect=generate, + ): + result = self._lint() + + assert any("out of date" in f for f in result["failed"]) + + def test_container_configs_missing_file(self): + """Linting fails when generate produces a config that has never been committed to the repo.""" + content = "process { withName: 'FASTQC' { container = 'docker.io/biocontainers/fastqc:0.12.1' } }\n" + + repo = git.Repo(self.new_pipeline) + repo.index.remove(["conf/containers_docker_amd64.config"], working_tree=True) + repo.index.commit("remove container config to simulate missing file") + + def generate(cc_self): + (cc_self.workflow_directory / "conf" / "containers_docker_amd64.config").write_text(content) + return {"containers_docker_amd64.config"} + + with patch( + "nf_core.pipelines.containers_utils.ContainerConfigs.generate_container_configs", + autospec=True, + side_effect=generate, + ): + result = self._lint() + + assert any("missing" in f for f in result["failed"]) + + def test_container_configs_fix_overwrites_files(self): + """--fix overwrites out-of-date container config files and reports them as fixed.""" + old = "process { withName: 'FASTQC' { container = 'old_image' } }\n" + new = "process { withName: 'FASTQC' { container = 'new_image' } }\n" + cfg = self._commit_container_cfg("containers_docker_amd64.config", old) + + def generate(cc_self): + (cc_self.workflow_directory / "conf" / "containers_docker_amd64.config").write_text(new) + return {"containers_docker_amd64.config"} + + with patch( + "nf_core.pipelines.containers_utils.ContainerConfigs.generate_container_configs", + autospec=True, + side_effect=generate, + ): + lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline, fix=("container_configs",)) + lint_obj._load() + result = lint_obj.container_configs() + + assert len(result["failed"]) == 0 + assert any("overwritten" in f for f in result["fixed"]) + assert cfg.read_text() == new + + def test_container_configs_user_warning_warns(self): + """A UserWarning from ContainerConfigs (e.g. low NF version) produces a lint warning.""" + with patch( + "nf_core.pipelines.containers_utils.ContainerConfigs.generate_container_configs", + autospec=True, + side_effect=UserWarning("Nextflow version too low"), + ): + result = self._lint() + + assert len(result["failed"]) == 0 + assert any("Nextflow version too low" in w for w in result["warned"]) diff --git a/tests/pipelines/test_container_configs.py b/tests/pipelines/test_container_configs.py new file mode 100644 index 0000000000..af9ab0064c --- /dev/null +++ b/tests/pipelines/test_container_configs.py @@ -0,0 +1,119 @@ +"""Tests for the ContainerConfigs helper used by pipelines.""" + +from pathlib import Path +from unittest.mock import patch + +import pytest +import ruamel.yaml + +from nf_core.modules.install import ModuleInstall +from nf_core.pipelines.containers_utils import PLATFORMS, ContainerConfigs +from nf_core.utils import NF_INSPECT_MIN_NF_VERSION, pretty_nf_version + +from ..test_pipelines import TestPipelines + +yaml = ruamel.yaml.YAML() + + +class TestContainerConfigs(TestPipelines): + """Tests for ContainerConfigs using a test pipeline.""" + + def setUp(self) -> None: + super().setUp() + self.container_configs = ContainerConfigs(self.pipeline_dir) + + def test_check_nextflow_version_sufficient_ok(self) -> None: + """check_nextflow_version should return silently when version is sufficient.""" + with patch( + "nf_core.pipelines.containers_utils.check_nextflow_version", + return_value=True, + ) as mocked_check: + self.container_configs.check_nextflow_version_sufficient() + + mocked_check.assert_called_once_with(NF_INSPECT_MIN_NF_VERSION, silent=True) + + def test_check_nextflow_version_sufficient_too_low(self) -> None: + """check_nextflow_version should raise UserWarning when version is too low.""" + with ( + patch( + "nf_core.pipelines.containers_utils.check_nextflow_version", + return_value=False, + ), + pytest.raises(UserWarning) as excinfo, + ): + self.container_configs.check_nextflow_version_sufficient() + + # Error message should mention the minimal required version + assert pretty_nf_version(NF_INSPECT_MIN_NF_VERSION) in str(excinfo.value) + + def test_generate_all_container_configs(self) -> None: + """Run generate_all_container_configs in a pipeline.""" + # Install fastqc and multiqc + mods_install = ModuleInstall( + self.pipeline_dir, prompt=False, force=False, sha="79b36b51048048374b642289bfe9e591ef56fe05" + ) + mods_install.install("fastqc") + mods_install.install("multiqc") + + self.container_configs.generate_container_configs() + + conf_dir = self.pipeline_dir / "conf" + with open(self.pipeline_dir / "modules" / "nf-core" / "fastqc" / "meta.yml") as fh: + fastqc_meta_yml = yaml.load(fh) + + for p_name, (runtime, arch, protocol) in PLATFORMS.items(): + cfg_path = conf_dir / f"containers_{p_name}.config" + assert cfg_path.exists() + with cfg_path.open("r") as fh: + content = fh.readlines() + value = fastqc_meta_yml["containers"][runtime][arch][protocol] + assert f"process {{ withName: 'FASTQC' {{ container = '{value}' }} }}\n" in content + + def test_generate_container_configs_new_module_injected(self) -> None: + """new_module_name/path are used when nextflow inspect doesn't yet know about the module.""" + mods_install = ModuleInstall( + self.pipeline_dir, prompt=False, force=False, sha="79b36b51048048374b642289bfe9e591ef56fe05" + ) + mods_install.install("fastqc") + + with open(self.pipeline_dir / "modules" / "nf-core" / "fastqc" / "meta.yml") as fh: + fastqc_meta_yml = yaml.load(fh) + + with ( + patch("nf_core.pipelines.containers_utils.check_nextflow_version", return_value=True), + patch( + "nf_core.pipelines.containers_utils.run_cmd", + return_value=('{"processes": []}', ""), + ), + ): + self.container_configs.generate_container_configs( + new_module_path=Path("modules/nf-core/fastqc"), + new_module_name="fastqc", + ) + + conf_dir = self.pipeline_dir / "conf" + for p_name, (runtime, arch, protocol) in PLATFORMS.items(): + cfg_path = conf_dir / f"containers_{p_name}.config" + assert cfg_path.exists() + value = fastqc_meta_yml["containers"][runtime][arch][protocol] + assert f"process {{ withName: 'FASTQC' {{ container = '{value}' }} }}\n" in cfg_path.read_text() + + def test_generate_container_configs_removes_stale_entries(self) -> None: + """Stale config files are deleted when all their modules have been removed.""" + conf_dir = self.pipeline_dir / "conf" + stale_line = "process { withName: 'REMOVED_MODULE' { container = 'stale/image:latest' } }\n" + for p_name in PLATFORMS: + (conf_dir / f"containers_{p_name}.config").write_text(stale_line) + + with ( + patch("nf_core.pipelines.containers_utils.check_nextflow_version", return_value=True), + patch( + "nf_core.pipelines.containers_utils.run_cmd", + return_value=('{"processes": []}', ""), + ), + ): + self.container_configs.generate_container_configs() + + for p_name in PLATFORMS: + cfg_path = conf_dir / f"containers_{p_name}.config" + assert not cfg_path.exists(), f"{cfg_path.name} should be deleted when all modules are removed"